Synthetic agonists of tlr9

ABSTRACT

The invention provides novel oligonucleotide-based compounds that individually provide distinct immune response profiles through their interactions as agonists with TLR9. The TLR9 agonists according to the invention are characterized by specific and unique chemical modifications, which provide their distinctive immune response activation profiles.

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser. No. 60/869,604, filed on Dec. 12, 2006, the contents of which are incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention relates to synthetic chemical compositions that are useful for modulation of Toll-Like Receptor (TLR)-mediated immune responses. In particular, the invention relates to agonists of Toll-Like Receptor 9 (TLR9) that generate unique cytokine and chemokine profiles.

2. Summary of the Related Art

Toll-like receptors (TLRs) are present on many cells of the immune system and have been shown to be involved in the innate immune response (Hornung, V. et al, (2002) J. Immunol. 168:4531-4537). In vertebrates, this family consists of eleven proteins called TLR1 to TLR11, which are known to recognize pathogen associated molecular patterns from bacteria, fungi, parasites, and viruses (Poltorak, a. et al. (1998) Science 282:2085-2088; Underhill, D. M., et al. (1999) Nature 401:811-815; Hayashi, F. et. al (2001) Nature 410:1099-1103; Zhang, D. et al. (2004) Science 303:1522-1526; Meier, A. et al. (2003) Cell. Microbiol. 5:561-570; Campos, M. A. et al. (2001) J. Immunol. 167: 416-423; Hoebe, K. et al. (2003) Nature 424: 743-748; Lund, J. (2003) J. Exp. Med. 198:513-520; Heil, F. et al. (2004) Science 303:1526-1529; Diebold, S. S., et al. (2004) Science 303:1529-1531; Hornung, V. et al. (2004) J. Immunol. 173:5935-5943).

TLRs are a key means by which vertebrates recognize and mount an immune response to foreign molecules and also provide a means by which the innate and adaptive immune responses are linked (Akira, S. et al. (2001) Nature Immunol. 2:675-680; Medzhitov, R. (2001) Nature Rev. Immunol. 1:135-145). Some TLRs are located on the cell surface to detect and initiate a response to extracellular pathogens and other TLRs are located inside the cell to detect and initiate a response to intracellular pathogens.

TLR9 is known to recognize unmethylated CpG motifs in bacterial DNA and in synthetic oligonucleotides. (Hemmi, H. et al. (2000) Nature 408:740-745). Other modifications of CpG-containing phosphorothioate oligonucleotides can also affect their ability to act as modulators of immune response through TLR9 (see, e.g., Zhao et al., Biochem. Pharmacol. (1996) 51:173-182; Zhao et al. (1996) Biochem Pharmacol. 52:1537-1544; Zhao et al. (1997) Antisense Nucleic Acid Drug Dev. 7:495-502; Zhao et al (1999) Bioorg. Med. Chem. Lett. 9:3453-3458; Zhao et al. (2000) Bioorg. Med. Chem. Lett. 10:1051-1054; Yu, D. et al. (2000) Bioorg. Med. Chem. Lett. 10:2585-2588; Yu, D. et al. (2001) Bioorg. Med. Chem. Lett. 11:2263-2267; and Kandimalla, E. et al. (2001) Bioorg. Med. Chem. 9:807-813). Naturally occurring agonists of TLR9 have been shown to produce anti-tumor activity (e.g. tumor growth and angiogenesis) resulting in an effective anti-cancer response (e.g. anti-leukemia) (Smith, J. B. and Wickstrom, E. (1998) J. Natl. Cancer Inst. 90:1146-1154). In addition, TLR9 agonists have been shown to work synergistically with other known anti-tumor compounds (e.g. cetuximab, irinotecan) (Vincenzo, D., et al. (2006) Clin. Cancer Res. 12(2):577-583).

Certain TLR9 agonists are comprised of 3′-3′ linked DNA structures containing a core CpR dinucleotide, wherein the R is a modified guanosine (U.S. patent application Ser. No. 10/279,684). In addition, specific chemical modifications have allowed the preparation of specific oligonucleotide analogs that generate distinct modulations of the immune response. In particular, structure activity relationship studies have allowed identification of synthetic motifs and novel DNA-based compounds that generate specific modulations of the immune response and these modulations are distinct from those generated by unmethylated CpG dinucleotides. (Kandimalla, E. et al. (2005) Proc. Natl. Acad. Sci. USA 102:6925-6930. Kandimalla, E. et al. (2003) Proc. Nat. Acad. Sci. USA 100:14303-14308; Cong, Y. et al. (2003) Biochem Biophys Res. Commun. 310:1133-1139; Kandimalla, E. et al. (2003) Biochem. Biophys. Res. Commun. 306:948-953; Kandimalla, E. et al. (2003) Nucleic Acids Res. 31:2393-2400; Yu, D. et al. (2003) Bioorg. Med. Chem. 11:459-464; Bhagat, L. et al. (2003) Biochem. Biophys. Res. Commun. 300:853-861; Yu, D. et al. (2002) Nucleic Acids Res. 30:4460-4469; Yu, D. et al. (2002) J. Med. Chem. 45:4540-4548. Yu, D. et al. (2002) Biochem. Biophys. Res. Commun. 297:83-90; Kandimalla. E. et al. (2002) Bioconjug. Chem. 13:966-974; Yu, D. et al. (2002) Nucleic Acids Res. 30:1613-1619; Yu, D. et al. (2001) Bioorg. Med. Chem. 9:2803-2808; Yu, D. et al. (2001) Bioorg. Med. Chem. Lett. 11:2263-2267; Kandimalla, E. et al. (2001) Bioorg. Med. Chem. 9:807-813; Yu, D. et al. (2000) Bioorg. Med. Chem. Lett. 10:2585-2588; Putta, M. et al. (2006) Nucleic Acids Res. 34:3231-3238).

The inventors have surprisingly discovered that unique modifications to the sequence flanking the core CpR dinucleotide produce novel agonists of TLR9 that generate distinct cytokine and chemokine profiles in vitro and in vivo. This ability to “custom-tune” the cytokine and chemokine response to a CpR containing oligonucleotide promises to provide the ability to prevent and/or treat various disease conditions in a disease-specific and even a patient-specific manner. Thus, there is a need for new oligonucleotide analog compounds to provide such custom-tuned responses.

BRIEF SUMMARY OF THE INVENTION

The invention provides novel oligonucleotide-based compounds that individually provide distinct immune response profiles through their interactions as agonists with TLR9. The TLR9 agonists according to the invention are characterized by specific and unique chemical modifications, which provide their distinctive immune response activation profiles.

The TLR9 agonists according to the invention induce immune responses in various cell types and in various in vitro and in vivo experimental models, with each agonist providing a distinct immune response profile. As such, they are useful as tools to study the immune system, as well as to compare the immune systems of various animal species, such as humans and mice. The TLR9 agonists according to the invention are also useful in the prevention and/or treatment of various diseases, either alone, in combination with other drugs, or as adjuvants for antigens used as vaccines.

Thus, in a first aspect, the invention provides oligonucleotide-based agonists of TLR9.

In a second aspect, the invention provides a composition comprising an oligonucleotide-based TLR9 agonist (“a compound”) according to the invention and a physiologically acceptable carrier.

In a third aspect, the invention provides a vaccine. Vaccines according to this aspect comprise a composition according to the invention, and further comprise an antigen.

In a fourth aspect, the invention provides methods for generating a TLR9-mediated immune response in a vertebrate, such methods comprising administering to the vertebrate a compound, composition or vaccine according to the invention.

In a fifth aspect, the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.

In a sixth aspect, the invention provides methods for preventing a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The invention provides novel oligonucleotide-based compounds that individually provide distinct immune response profiles through their interactions as agonists with TLR9. The TLR9 agonists according to the invention are characterized by unique chemical modifications, which provide their distinctive immune response activation profiles. All publications cited herein reflect the level of skill in the art and are hereby incorporated by reference in their entirety. Any conflict between the teachings of these references and this specification shall be resolved in favor of the latter.

The TLR9 agonists according to the invention induce immune responses in various cell types and in various in vivo and in vitro experimental models, with each agonist providing a distinct immune response profile. As such, they are useful as tools to study the immune system, as well as to compare the immune systems of various animal species, such as humans and mice. The TLR9 agonists according to the invention are also useful in the prevention and/or treatment of various diseases, either alone, in combination with other drugs, or as adjuvants for antigens used as vaccines.

Certain TLR9 agonists according to the invention are shown in Table I below. In this table, the oligonucleotide-based TLR9 agonists have all phosphorothioate (PS) linkages, except where indicated. Except where indicated, all nucleotides are deoxyribonucleotides. Those skilled in the art will recognize, however, that phosphodiester (PO) linkages, or a mixture of PS and PO linkages can be used.

TABLE I Seq. ID. No./ Oligo No. Sequence and Modifications 1 5′-TCAGTCG1TTAC-X-CATTG1CTGACT-5′ 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTGCT-5′ 11 5′-TCG ₁TACG ₁TACG ₁-X-G ₁CATG ₁CATG ₁CT-5′ 12 5′-TCG ₁TCG ₁ACG ₁AT-X-TAG ₁CAG ₁CTG ₁CT-5′ 13 5′-TCG ₁ATCG ₁ATCG ₁-X-G ₁CTAG ₁CTAG ₁CT-5′ 14 5′-TCAGACG ₁TTAC-X-CATTG ₁CAGACT-5′ 15 5′-TCTGACG ₁TTAG-X-GATTG ₁CAGTCT-5′ 16 5′-CAGACG ₁TTCAG-X-GACTTG ₁CAGAC-5′ 17 5′-TCTGACG ₁TTTT-X-TTTTG ₁CAGTCT-5′ 18 5′-TCTGACGTTGT-X-TGTTG ₁CAGTCT-5′ 19 5′-TAGACG ₁TTTTT-X-TTTTTG ₁CAGAT-5′ 20 5′-TGGACG ₁TTCTT-X-TTCTTG ₁CAGGT-5′ 21 5′-TAGACGTTGTA-X-ATGTTG ₁CAGAT-5′ 22 5′-TAGACG ₁TTCTC-X-CTCTTG ₁CAGAT-5′ 23 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 31 5′-TAGTCG ₂TGTA-X-ATGTTG ₂CTGAT-5′ 32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 37 5′-TCTGTCGTTCT-Y-TCTTGCTGTCT-5′ 38 5′-TCTGACG ₁TTCT-Y-TCTTG ₁CAGTCT-5′ 39 5′-TCG ₁AACG ₁TTCG ₁-Y-G ₁CTTG ₁CAAG ₁CT-5′ 40 5′-TCG ₁TCG ₁TTCTG-Y-GTCTTG ₁CTG ₁CT-5′ 41 5′-TCAGTC ₁GTTAG-Y-GATTGC ₁TGACT-5′ 42 5′-TCTGTC ₁GTTCT-Y-TCTTGC ₁TGTCT-5′ 43 5′-TCGTTGL-Y-LGTTGCT-5′ 44 5′-TCGTTGM-Y-MGTTGCT-5′ 45 5′-TCG ₁TTGM-Y-MGTTG ₁CT-5′ 46 5′-TCGTTGM-X-MGTTGCT-5′ 47 5′-TCG ₁AACG ₁TTCG ₁-M-TCTTG ₁CTGTCT-5′ 48 5′-TCG ₁AACG ₁TTCG ₁-M-GACAG ₁CTGTCT-5′ 49 [(5′-TCTGACG ₁TTCT)₂Y]₂Y 50 5′-TCTGTCG ₃TTCT-Y-TCTTG ₃CTGTCT-5′ 51 5′-TCTGACG ₃TTCT-Y-TCTTG ₃CAGTCT-5′ 52 5′-TCTGTC ₁ G ₃TTCT-Y-TCTTG ₃ C ₁TGTCT-5′ 53 5′-TCTGACGTTCT-Z-TCTTGCAGTCT-5′ 54 5′-TCTGACG ₁TTCT-Z-TCTTG ₁CAGTCT-5′ 55 5′-TCTGTCG ₁TTCT-Z-TCTTG ₁CTGTCT-5′ 56 5′-TCTGACG ₁TTCT-S-TCTTG ₁CAGTCT-5′ 57 5′-TCTGTCG ₁TTCT-S-TCTTG ₁CTGTCT-5′ 58 5′-TCG ₁AACG ₁TTCG ₁-S-G ₁CTTG ₁CAAG ₁CT-5′ 59 5′-TCAGTCG ₁TTAG-S-GATTG ₁CTGACT-5′ 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTGTCT-5′ 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CTGAC-5′ 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CAG ₁CTG ₁CT-5′ 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 76 5′-TCAoGToCG ₂TTAC-X-CATTG ₂CoTGoACT-5′ 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTA T-5′ 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoTo G ₂CT-5′ 83 5′-TCG ₂AoToCG ₂oAoTCG ₂-X-G ₂CToAoG ₂CoTo AG ₂CT-5′ 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CT-5′ 87 5′-LTCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CTL-5′ 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CTG ₁CTL-5′ 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 91 5′-LTCG ₁TCG ₁TTL-X-LTTTG ₁CTG ₁CTL-5′ 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ G ₁ = 7-deaza-dG; G ₂ = AraG; G ₃ = N¹-Me-dG; C ₁ = 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine; U / C / G / A  =2′-O-methylribonucleotides; o = phosphodiester linkage; X = Glycerol; Y = 1,3,5-Pentanetriol; L = 1,3-Propanediol; M = 1,5-Pentanediol; Z = cis,cis-1,3,5-Cyclohexanetriol; S = 3-Me-1,3,5-pentanetriol

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in HEK293 cells expressing TLR9, as described in Example 2. The results shown in Table II(a), II(b), II(c), and II(d) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated NF-kB activation profile 24 hours after administration. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease NF-kB activation.

TABLE II(a) NF-kB Activation Profiles in HEK293 Cells Expressing TLR9 Fold Changes Seq. ID. in NF-kB No./ Sequences and Modification Activity ± SD Oligo No. (5′-3′) at 10 μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTG 13.94 ± 0.33  ACT-5′ 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTG 6.76 ± 0.12 TCT-5′ 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CT 10.45 ± 0.13  GAC-5′ 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTG 7.84 ± 0.02 TCT-5′ 5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTG 9.45 ± 1.31 TCT-5′ 6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CG 6.95 ± 0.05 TAT-5′ 7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CT 5.02 ± 0.13 GGT-5′ 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CT 2.75 ± 0.46 GAT-5′ 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CT 12.59 ± 0.26  GAT-5′ 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁C 13.24 ± 1.58  TG ₁CT-5′ 14 5′-TCAGACG ₁TTAC-X-CATTG ₁CAG 14.32 ± 0.19  ACT-5′ 15 5′-TCTGACG ₁TTAG-X-GATTG ₁CAG 12.19 ± 0.94  TCT-5′ 16 5′-CAGACG ₁TTCAG-X-GACTTG ₁CA 16.42 ± 0.44  GAC-5′ 17 5′-TCTGACG ₁TTTT-X-TTTTG ₁CAG 16.49 ± 1.13  TCT-5′ 18 5′-TCTGACG ₁TTGT-X-TGTTG ₁CAG 14.63 ± 0.03  TCT-5′ 19 5′-TAGACG ₁TTTTT-X-TTTTTG ₁CA 16.06 ± 0.71  GAT-5′ 20 5′-TGGACG ₁TTCTT-X-TTCTTG ₁CA 13.28 ± 0.42  GGT-5′ 21 5′-TAGACG ₁TTGTA-X-ATGTTG ₁CA 11.75 ± 0.42  GAT-5′ 22 5′-TAGACG ₁TTCTC-X-CTCTTG ₁CA 13.70 ± 0.21  GAT-5′ Media    1 ± 0.07

TABLE II(b) NF-kB Activation Profiles in HEK293 Cells Expressing TLR9 Fold Changes Seq. ID. in NF-kB No./ Sequences and Modification Activity Oligo No. (5′-3′) at 10 μg/ml 37 5′-TCTGTCGTTCT-Y-TCTTGCTGTC 11.35 T-5′ 38 5′-TCTGACG ₁TTCT-Y-TCTTG ₁CAG 11.51 TCT-5′ 50 5′-TCTGTCG ₃TTCT-Y-TCTTG ₃CTG 12.32 TCT-5′ 52 5′-TCTGTCG ₃TTCT-Y-TCTTG ₃CTG 9.40 TCT-5′ 57 5′-TCTGTCG ₁TTCT-S-TCTTG ₁CTG 11.05 TCT-5′ PBS 1.00

TABLE II(c) NF-kB Activation Profiles in HEK293 Cells Expressing TLR9 Fold Changes Seq. ID. in NF-κB No./ Sequences and Modification Activity ± Oligo No. (5′-3′) SD at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁C 11.2 ± 0.06 TGTCT-5′ 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TT  9.5 ± 0.06 G ₁CTGTCT-5′ 62 5′-TCTGTCG ₂TTb CU-X- UC TTG ₂CTG  6.6 ± 0.04 TCT-5′ 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CT 14.6 ± 0.09 GTC-5′ 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CA 32.1 ± 0.6  AG ₁CT-5′ 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁C 23.7 ± 0.2  TGTCT-5′ PBS    1 ± 0.03

TABLE II(d) NF-kB Activation Profiles in HEK293 Cells Expressing TLR9 Fold Changes Seq. ID. in NF-κB No./ Sequences and Modification Activity ± Oligo No. (5′-3′) SD at 10 μg/ml 72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTG 3.81 ± 0.14 TCT-5′ 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CT 5.47 ± 0.17 GAC-5′ 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CA  9.46 ± 1.35; G ₁CTG ₁CT-5′ 9.18 ± 0.09 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTG  5.08 ± 0.58; ACT-5′ 6.91 ± 1.52 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTG  5.33 ± 0.25; AC U -5′ 4.85 ± 0.46 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁C  7.63 ± 0.54; TGACT-5′ 10.7 ± 90.9 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂  5.63 ± 1.46; CoTGTAT-5′ 5.75 ± 0.45 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂Co  9.60 ± 1.39; TGTCT-5′ 9.75 ± 0.25 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂  5.63 ± 0.46; CoToGTAT-5′ 6.22 ± 0.12 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂  9.71 ± 0.75; CoAG ₂CoToG ₂CT-5′ 12.5 ± 90.3 83 5′-TCG ₂AoToCG ₂oAoTCG ₂-X-G ₂C 7.24 ± 0.42 ToAoG ₂CoToAG ₂CT-5′ 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂Co  8.92 ± 0.88; TGACT-5′ 10.33 ± 0.2;  12.16 ± 1.5   85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂Co  9.13 ± 1.25; ToGTCT-5′  8.05 ± 0.39; 11.3 ± 40.3 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CT 11.6 ± 10.6 G ₁CT-5′ 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁  9.61 ± 0.14; CT-5′ 9.32 ± 0.20 89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CT 2.57 ± 0.28 G ₁CTL-5′ 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CT  9.65 ± 1.78; G ₁CT-5′ 9.57 ± 0.18 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTG  5.67 ± 0.25; A C T-5′ 7.25 ± 1.23 Media   1.0 ± 0.17;     1 ± 0.25;   1.0 ± 0.02;  1.0 ± 0.11

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the C57BL/6 mouse spleenocyte IL-12 assay, as described in Example 3. The results shown in Table III(a), III(b) and III(c) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IL-12 activation profile in spleen cells 24 hours after administration and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IL-12 activation.

TABLE III(a) Induction of IL-12 Secretion in C57BL/6 Mouse Spleen Cell Cultures Seq. ID. No./ IL-12 (pg/m ± SD1) Oligo No. Sequences and Modification (5′-3′) at 1 μg/ml at 3 μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 733 ± 5   638 ± 14  2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 919 ± 8   660 ± 8   3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 500 ± 26  634 ± 49  4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 822 ± 9   516 ± 7   5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 636 ± 6   369 ± 4   6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 857 ± 0   115 ± 0   7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 61 ± 0  357 ± 16  8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 253 ± 10  120 ± 13  9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 743 ± 33  553 ± 12  10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 714 ± 0   913 ± 12  14 5′-TCAGACG ₁TTAC-X-CATTG ₁CAGACT-5′ 1654 ± 64   1592 ± 27   15 5′-TCTGACG ₁TTAG-X-GATTG ₁CAGTCT-5′ 1299 ± 2    1257 ± 8    16 5′-CAGACG ₁TTCAG-X-GACTTG ₁CAGAC-5′ 1152 ± 11   1134 ± 0    17 5′-TCTGACG ₁TTTT-X-TTTTG ₁CAGTCT-5′ 1370 ± 4    1015 ± 7    18 5′-TCTGACG ₁TTGT-X-TGTTG ₁CAGTCT-5′ 1140 ± 16   816 ± 4   19 5′-TAGACG ₁TTTTT-X-TTTTTG ₁CAGAT-5′ 1215 ± 32   719 ± 3   20 5′-TGGACG ₁TTCTT-X-TTCTTG ₁CAGGT-5′ 814 ± 9   645 ± 40  21 5′-TAGACG ₁TTGTA-X-ATGTTG ₁CAGAT-5′ 835 ± 34  750 ± 16  22 5′-TAGACG ₁TTCTC-X-CTCTTG ₁CAGAT-5′ 1211 ± 26   898 ± 24  Media 154 ± 1   154 ± 1  

TABLE III(b) Induction of IL-12 Secretion in C57BL/6 Mouse Spleen Cell Cultures Seq. ID. No./ Oligo No. Sequences and Modifications (5′-3′) IL-12 (pg/ml ± SD) 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 932 ± 18  892 ± 2   25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 771 ± 6  604 ± 6   26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 835 ± 4   905 ± 4   27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 571 ± 11  502 ± 2   28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 567 ± 0   698 ± 77  29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 975 ± 24  656 ± 33  30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 426 ± 16  393 ± 1   31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 568 ± 23  575 ± 14  32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 960 ± 2   647 ± 13  33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 659 ± 10 1014 ± 1    34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 1044 ± 66   1109 ± 32   35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 1406 ± 36   968 ± 4   36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 912 ± 3   1035 ± 11   media 190 ± 4  

TABLE III(c) Induction of IL-12 Secretion in C57BL/6 Mouse Spleen Cell Cultures Seq. ID. No./ IL-12 Oligo No. Sequences and Modification (5′-3′) (pg/ml ± SD) 72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTGTCT-5′  988 ± 224 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CTGAC-5′ 504 ± 76 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CAG ₁CTG ₁CT-5′ 906 ± 47 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 473 ± 67 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 265 ± 19 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 833 ± 63 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 380 ± 54 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 1502 ± 162 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 370 ± 47 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 1599 ± 156 83 5′-TCG ₂AoToCG ₂oAoTCG ₂-X-G ₂CToAoG ₂CoToAG ₂CT-5′ 1203 ± 109 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 838 ± 61 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 589 ± 45 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CT-5′ 1603 ± 167 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 1643 ± 40  89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CTG ₁CTL-5′ 450 ± 50 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 1393 ± 9   92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 383 ± 23 Media  82 ± 4; 168 ± 15

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the C57BL/6 mouse spleenocyte IL-6 assay, as described in Example 3. The results shown in Table IV(a), IV(b), and IV(c) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IL-6 activation profile in spleen cells 24 hours after administration and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IL-6 activation.

TABLE IV(a) Induction of IL-6 Secretion in C57BL/6 Mouse Spleen Cell Cultures Seq. ID. No./ IL-6 (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 1 μg/ml at 3 μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 2436 ± 93   6282 ± 138  2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 1812 ± 95   5758 ± 55   3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 1650 ± 63   3349 ± 46   4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 707 ± 59  7018 ± 3    5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 1302 ± 56   5874 ± 83   6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 1025 ± 93   1677 ± 12   7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 453 ± 8   3068 ± 3    8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 914 ± 74  1147 ± 30   9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 3570 ± 21   12114 ± 86    10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 77 ± 0  1657 ± 17   14 5′-TCAGACG ₁TTAC-X-CATTG ₁CAGACT-5′ 2605 ± 15   7206 ± 16  15 5′-TCTGACG ₁TTAG-X-GATTG ₁CAGTCT-5′ 1705 ± 28   6538 ± 63  16 5′-CAGACG ₁TTCAG-X-GACTTG ₁CAGAC-5′ 1081 ± 20   3765 ± 18   17 5′-TCTGACG ₁TTTT-X-TTTTG ₁CAGTCT-5′ 1711 ± 32   8386 ± 33   18 5′-TCTGACG ₁TTGT-X-TGTTG ₁CAGTCT-5′ 1725 ± 0    7340 ± 142  19 5′-TAGACG ₁TTTTT-X-TTTTTG ₁CAGAT-5′ 984 ± 16  3312 ± 22   20 5′-TGGACG ₁TTCTT-X-TTCTTG ₁CAGGT-5′ 515 ± 77  1828 ± 22   21 5′-TAGACG ₁TTGTA-X-ATGTTG ₁CAGAT-5′ 221 ± 5   1539 ± 9    22 5′-TAGACG ₁TTCTC-X-CTCTTG ₁CAGAT-5′ 1593 ± 19   6960 ± 81   Media 0 ± 0 0 ± 0

TABLE IV(b) Induction of IL-6 Secretion in C57BL/6 Mouse Spleen Cell Cultures (24 hours) Seq. ID. No./ Oligo No. Sequences and Modifications (5′-3′) IL-6 (pg/ml ± SD) 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 8276 ± 35   11634 ± 83    25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 5428 ± 106  11860 ± 154   26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 6389 ± 15   12402 ± 77    27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 3977 ± 89   8058 ± 46   28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 4333 ± 59   10555 ± 49    29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 3380 ± 24   9348 ± 90   30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 2452 ± 45   4028 ± 15   31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 2574 ± 45   6426 ± 40   32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 6432 ± 4    10872 ± 413   33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 6136 ± 24   10408 ± 7     34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 7840 ± 61   15642 ± 56    35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 8004 ± 141  15174 ± 54    36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 5590 ± 259  14788 ± 441   media 346 ± 0  

TABLE IV(c) Induction of IL-6 Secretion in C57BL/6 Mouse Spleen Cell Cultures (24 hours) Seq. ID. No./ IL-6 Oligo No. Sequences and Modification (5′-3′) (pg/ml ± SD) 72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTGTCT-5′  8388 ± 1609 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CTGAC-5′  4198 ± 1602 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CAG ₁CTG ₁CT-5′ 18828 ± 1448 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 3689 ± 109 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′  91 ± 12 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 22047 ± 8443 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 1234 ± 508 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 1402 ± 5369 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 373 ± 61 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 86355 ± 4638 83 5′-TCG ₂AoToCG ₂oAoTCG ₂-X-G ₂CToAoG ₂CoToAG ₂CT-5′ 10871 ± 1996 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 30346 ± 1670 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 113 ± 11 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CT-5′ 15654 ± 470  88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 16317 ± 659  89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CTG ₁CTL-5′ 1259 ± 215 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 13864 ± 344  92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 2171 ± 186 Media  51 ± 3; 60 ± 1

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human B-cell proliferation assay, as described in Example 4. The results shown in Table V(a), V(b), V(c), V(d) and V(e) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated B-cell proliferation activity and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to regulate B-cell proliferation.

TABLE V(a) Human B-Cell Proliferation Assay Seq. ID. No./ Sequences and Modification [³H]-T (cpm ± SD) Oligo No. (5′-3′) at 1 μg/ml at 3 μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 9170 ± 5038 7556 ± 3260 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 9907 ± 4299 9405 ± 3319 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 7594 ± 4088 7094 ± 1526 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 13130 ± 6721  12343 ± 4336  5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 11990 ± 5511  12102 ± 5618  6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 13676 ± 3676  14223 ± 6073  7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 7286 ± 2800 7007 ± 1424 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 7858 ± 2877 8757 ± 3733 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 7834 ± 2397 6840 ± 2158 Media 559 ± 355 559 ± 355

TABLE V(b) Human B-Cell Proliferation Assay Seq. ID. No./ Oligo No. Sequences and Modification (5′-3′) [³H]-T (cpm ± SD) 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 12015 ± 2721  22634 ± 7474  25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 12033 ± 1502  28048 ± 14380 26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 8738 ± 2957 23675 ± 11455 27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 17623 ± 4158  24309 ± 7340  28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 13631 ± 1735  18438 ± 3212  29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 12051 ± 5367  19867 ± 9831  30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 17206 ± 8474  18061 ± 9703  31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 21600 ± 10694 22746 ± 13411  32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 15827 ± 8603  26722 ± 16455 33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 19269 ± 14059 21945 ± 11281 34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 11228 ± 4499  17990 ± 7547  35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 13364 ± 2570  22787 ± 3265  36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 14071 ± 3313  31519 ± 2373  media 634 ± 166

TABLE V(c) Human B-Cell Proliferation Assay Seq. ID. No./ Oligo No. Sequences and Modification (5′-3′) [³H]-T (cpm ± SD) 38 5′-TCTGACG ₁TTCT-Y-TCTTG ₁CAGTCT-5′ 4714 ± 1043 4535 ± 1269 39 5′-TCG ₁AACG ₁TTCG ₁-Y-G ₁CTTG ₁CAAG ₁CT-5′ 3664 ± 219  7556 ± 1615 40 5′-TCG ₁TCG ₁TTCTG-Y-GTCTTG ₁CTG ₁CT-5′ 4346 ± 453  6093 ± 2052 41 5′-TCAGTCGTTAG-Y-GATTGCTGACT-5′ 3585 ± 495  4371 ± 1380 42 5′-TCTGTCGTTCT-Y-TCTTGCTGTCT-5′ 5607 ± 1163 5202 ± 1980 43 5′-TCGTTGL-Y-LGTTGCT-5′ 3302 ± 359  4767 ± 737  47 5′-TCG ₁AACG ₁TTCG ₁-M-TCTTG ₁CTGTCT-5′ 6010 ± 1951 6469 ± 3332 48 5′-TCG ₁AACG ₁TTCG ₁-M-GACAG ₁CTGTCT-5′ 3507 ± 768  4351 ± 2101 PBS 545 ± 237

TABLE V(d) Human B-Cell Proliferation Assay Seq. ID. Proliferation No./ Index Oligo No. Sequences and Modification (5′-3′) at 1 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 28.4 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 31.3 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 42.6 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 41.5 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 45.6 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 23.8 Medium 1

TABLE V(e) Human B-Cell Proliferation Assay Seq. ID. Proliferation No./ Index Oligo No. Sequences and Modification (5′-3′) at 1 μg/ml 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 13582 ± 1296 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 19250 ± 1860 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 24809 ± 3983 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 21125 ± 2056 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 20306 ± 6796 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 11547 ± 631  72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTGTCT-5′ 16603 ± 2124 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CTGAC-5′  9787 ± 1290 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CAG ₁CTG ₁CT-5′ 16934 ± 2628 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 16347 ± 980 18093 ± 3142 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 14546 ± 2616 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 10051 ± 1376 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CT-5′ 18297 ± 1246 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′  12128 ± 2106 16534 ± 1037 89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CTG ₁CTL-5′ 10749 ± 1191 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 11357 ± 692; 22666 ± 54   91 5′-LTCG ₁TCG ₁TTL-X-LTTTG ₁CTG ₁CTL-5′ 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ Media  621 ± 215

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC and B-Cell assays for IL-1Ra, IL-6, IL-10, and IL-12, as described in Example 3. The results shown in Table VI(a), VI(b), VI(c), VI(d), VI(e), VI(f), VI(g), and VI(h) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IL-1Rα, IL-6, IL-10, and/or IL-12 activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IL-1Rα, IL-6, IL-10, and IL-12 activation.

TABLE VI(a) Human PBMC Assay for IL-1Rα, IL-6 and IL-12 IL-1Rα IL-6 IL-12 Seq. ID. (pg/ml) (pg/ml) (pg/ml) No./ at 10 at 10 at 10 Oligo No. Sequences and Modification (5′-3′) μg/ml μg/ml μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 1331 1035 116.5 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 599.5 630 56.5 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 1133 867.5 76 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 926 994 81 5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 874.5 813.5 69 6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 921 958 90.5 7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 1365 1110.5 101.5 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 744 1048.5 75.5 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 1239 1084.5 104.5 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 1727 1415.5 145 11 5′-TCG ₁TACG ₁TACG ₁-X-G ₁CATG ₁CATG ₁CT-5′ 2905.5 2099.5 197.5 12 5′-TCG ₁TCG ₁ACG ₁AT-X-TAG ₁CAG ₁CTG ₁CT-5′ 2965 1985.3 192.7 13 5′-TCG ₁ATCG ₁ATCG ₁-X-G ₁CTAG ₁CTAG ₁CT-5′ 3584.5 2543.5 300.5 Media 187 36 21

TABLE VI(b) Human PBMC Assay for IL-1Rα, IL-6 and IL-12 IL-1Rα IL-6 IL-12 Seq. ID. (pg/ml) (pg/ml) (pg/ml) No./ at 10 at 10 at 10 Oligo No. Sequences and Modification (5′-3′) μg/ml μg/ml μg/ml 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 10537.8 340.8 350.7 25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 14850.4 413.6 456.1 26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 9440.6 335.0 304.4 27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 13014.5 499.0 421.9 28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 10270.2 363.2 323.0 29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 11644.7 421.2 362.3 30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 10528.9 465.7 339.2 31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 19086.4 554.6 551.3 32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 15514.6 434.8 462.9 33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 22655.8 551.9 598.6 34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 20375.5 456.3 596.3 35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 17750.6 383.5 521.9 36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 23576.8 428.0 706.3 media 799.5 15.7 47.7

TABLE VI(c) Human PBMC Assay for IL-6 (24 hours) Seq. ID. No./ IL-6 (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 423 ± 1 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′  938 ± 14 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 497 ± 4 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 409 ± 2 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 474 ± 0 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 626 ± 3 Medium   0 ± 0

TABLE VI(d) Human PBMC Assay for IL-6 (24 hours) Seq. ID. IL-6 No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 135.63 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 117.98 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 300.79 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 151.84 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 268.71 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 364.23 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 722.58 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 615.21 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 449.96 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 658.10 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 490.37 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 668.52 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 614.15 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 603.68; 351.00 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 387.97; 464.58 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 440.25 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 446.67 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 605.79 Media 7.12; 3.59

TABLE VI(e) Human PBMC Assay for IL-10 (24 hours) Seq. ID. IL-10 No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 44 ± 6 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 50 ± 6 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 42 ± 2 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 55 ± 2 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 11 ± 2 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 26 ± 2 Medium 18 ± 0

TABLE VI(f) Human PBMC Assay for IL-12 (24 hours) Seq. ID. IL-12 No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 284.03 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 296.62 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 502.12 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 531.48 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 729.32 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 810.12 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 1678.61 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 1500.97 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 927.15 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 1013.11 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 1498.64 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 1019.68 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 1220.94 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 1450.24; 1604.88 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 879.09; 1498.64 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 1463.20 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 1417.50 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 1602.41 Media 54.36; 196.06; 511.18

TABLE VI(g) Induction of IL-6 in human B cell cultures (24 hours) Seq. ID. IL-6 No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 359 ± 7  61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 570 ± 37 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 333 ± 3  63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 593 ± 8  64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 503 ± 28 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 481 ± 13 Medium 91 ± 0

TABLE VI(h) Induction of IL-10 in human B cell cultures (24 hours) Seq. ID. IL-10 No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 188 ± 0 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 286 ± 3 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′  223 ± 10 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 201 ± 2 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 268 ± 0 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 212 ± 1 Medium  86 ± 5

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC assay for IFN-γ, MIP-1α and MIP-β, as described in Example 3. The results shown in Table VII(a) and VII(b) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IFN-γ, MIP-1α, and/or MIP-β activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IFN-γ, MIP-1α, and MIP-β activation.

TABLE VII(a) Human PBMC Assay for IFN-γ, MIP-1α and MIP-β IFN-γ MIP-1α MIP-β Seq. ID. (pg/ml) (pg/ml) (pg/ml) No./ at 10 at 10 at 10 Oligo No. Sequences and Modification (5′-3′) μg/ml μg/ml μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 86 28 1108 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 38.5 11 568.5 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 29 8.5 465.5 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 31.5 14 648.5 5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 52.5 12 679 6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 66.5 15.5 799 7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 68.5 17 889.5 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 77 20 1174 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 93.5 26.5 1240.5 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 59.5 29.5 1007 11 5′-TCG ₁TACG ₁TACG ₁-X-G ₁CATG ₁CATG ₁CT-5′ 5237.5 83 2931.5 12 5′-TCG ₁TCG ₁ACG ₁AT-X-TAG ₁CAG ₁CTG ₁CT-5′ 2199.7 24.7 2363 13 5′-TCG ₁ATCG ₁ATCG ₁-X-G ₁CTAG ₁CTAG ₁CT-5′ 5619.5 173 2479 Media 40 6 187

TABLE VII(b) Human PBMC Assay for IFN-γ, MIP-1α and MIP-β IFN-γ MIP-1α MIP-β Seq. ID. (pg/ml) (pg/ml) (pg/ml) No./ at 10 at 10 at 10 Oligo No. Sequences and Modification (5′-3′) μg/ml μg/ml μg/ml 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 11.29 84.49 1373.07 25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 14.44 90.61 1557.81 26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 11.29 84.49 1337.00 27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 13.66 109.05 1746.19 28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 12.08 87.58 1337.01 29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 12.87 82.12 1428.54 30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 11.29 105.04 1839.64 31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 13.66 113.18 1995.04 32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 12.08 107.78 1603.54 33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 13.66 150.26 2785.79 34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 13.66 195.82 3966.88 35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 10.50 134.83 2878.33 36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 8.11 107.78 2343.94 media 3.25 6.11 149.2

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC assay for MCP-1 and IFN-α, as described in Example 3. The results shown in Table VIII(a) and VIII(b) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated MCP-1 and/or IFN-α activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease MCP-1 and IFN-α activation.

TABLE VIII(a) Human PBMC Assay for MCP-1 and IFN-α Seq. ID. MCP-1 IFN-α No./ (pg/ml) (pg/ml) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml at 10 μg/ml 1 5′-TCAGTCG ₁TTAC-X-CATTG ₁CTGACT-5′ 3774.5 86 2 5′-TCTGTCG ₁TTAG-X-GATTG ₁CTGTCT-5′ 841 38.5 3 5′-CAGTCG ₁TTCAG-X-GACTTG ₁CTGAC-5′ 3503 29 4 5′-TCTGTCG ₁TTTT-X-TTTTG ₁CTGTCT-5′ 2514 31.5 5 5′-TCTGTCG ₁TTGT-X-TGTTG ₁CTGTCT-5′ 2134.5 52.5 6 5′-TAGTCG ₁TTTTT-X-TTTTTG ₁CGTAT-5′ 2154 66.5 7 5′-TGGTCG ₁TTCTT-X-TTCTTG ₁CTGGT-5′ 4201.5 68.5 8 5′-TAGTCG ₁TTGTA-X-ATGTTG ₁CTGAT-5′ 3620 77 9 5′-TAGTCG ₁TTCTC-X-CTCTTG ₁CTGAT-5′ 4885 935 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 2672 59.5 11 5′-TCG ₁TACG ₁TACG ₁-X-G ₁CATG ₁CATG ₁CT-5′ 6793 5237.5 12 5′-TCG ₁TCG ₁ACG ₁AT-X-TAG ₁CAG ₁CTG ₁CT-5′ 6251 2199.7 13 5′-TCG ₁ATCG ₁ATCG ₁-X-G ₁CTAG ₁CTAG ₁CT-5′ 6686 5619.5 Media 534 40

TABLE VIII(b) Human PBMC Assay for MCP-1 and IFN-α Seq. ID. MCP-1 IFN-α No./ (pg/ml) (pg/ml) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml at 10 μg/ml 24 5′-TCAGTCG ₂TTAC-X-CATTG ₂CTGACT-5′ 12480.44 62.03 25 5′-TCTGTCG ₂TTAG-X-GATTG ₂CTGTCT-5′ 50410.30 18.07 26 5′-CAGTCG ₂TTCAG-X-GACTTG ₂CTGAC-5′ 3982.45 42.09 27 5′-TCTGTCG ₂TTTT-X-TTTTG ₂CTGTCT-5′ 53685.37 13.28 28 5′-TCTGTCG ₂TTGT-X-TGTTG ₂CTGTCT-5′ 6116.14 46.03 29 5′-TAGTCG ₂TTTTT-X-TTTTTG ₂CGTAT-5′ 26435.31 38.08 30 5′-TGGTCG ₂TTCTT-X-TTCTTG ₂CTGGT-5′ 12012.62 30.38 31 5′-TAGTCG ₂TTGTA-X-ATGTTG ₂CTGAT-5′ 53166.41 26.16 32 5′-TAGTCG ₂TTCTC-X-CTCTTG ₂CTGAT-5′ 36199.26 67.03 33 5′-TCG ₂TCG ₂TTCTT-X-TTCTTG ₂CTG ₂CT-5′ 42397.84 31.4 34 5′-TCG ₂TACG ₂TACG ₂-X-G ₂CATG ₂CATG ₂CT-5′ 62106.60 83.69 35 5′-TCG ₂TCG ₂ACG ₂AT-X-TAG ₂CAG ₂CTG ₂CT-5′ 41760.82 29.94 36 5′-TCG ₂ATCG ₂ATCG ₂-X-G ₂CTAG ₂CTAG ₂CT-5′ 25530.72 942.37 media 267.37 0

Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC and pDC assays for IFN-α, IL6, and IL-12, as described in Example 3. The results shown in Table IX(a), IX(b), IX(c), IX(d), IX(e), IX(f), and IX(g) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IFN-α activation profile in human PBMCs and pDCs. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IFN-α, IL-6, and IL-12 activation.

TABLE IX(a) Human PBMC Assay for IFN-α Seq. ID. IFN-α No./ (pg/ml) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 10 5′-TCG ₁TCG ₁TTCTT-X-TTCTTG ₁CTG ₁CT-5′ 142.5 11 5′-TCG ₁TACG ₁TACG ₁-X-G ₁CATG ₁CATG ₁CT-5′ 8065.5 12 5′-TCG ₁TCG ₁ACG ₁AT-X-TAG ₁CAG ₁CTG ₁CT-5′ 7270.5 13 5′-TCG ₁ATCG ₁ATCG ₁-X-G ₁CTAG ₁CTAG ₁CT-5′ 8437 Media 109.5

TABLE IX(b) Human PBMC Assay for IFN-α (24 hours)^(a) Seq. ID. IFN-α No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 257.5 ± 539.4 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 39.0 ± 88.5 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′  84.4 ± 143.2 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 34.0 ± 37.1 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 1165 ± 704.7 65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 2494.3 ± 1880.1 Medium 22.2 ± 39.8 ^(a)Data are mean of 10 donors

TABLE IX(c) Human PBMC Assay for IFN-α (24 hours) Seq. ID. No./ IFN-α (pg/ml) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 53.42 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 56.30 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 622.25 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 1823.24 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 97.42 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 92.64 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 86.38 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 86.38 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 66.13 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 92.10 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 65.86 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 86.38; 761.92 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 98.37; 592.17 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 958.92 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 710.90 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 92.64 Media 32.9; 64.8; 14.5

TABLE IX(d) Human pDC Assay for IFN-α (24 hours)^(a) Seq. ID. IFN-α No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 1509.5 ± 2612.7 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 1598.9 ± 3727.2 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 3415.6 ± 3903.6 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′ 2180.1 ± 3882.0 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 32956.8 ± 2639.9  65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 47746.2 ± 53192.1 Medium 106.6 ± 156.5 ^(a)Data are mean of 10 donors

TABLE IX(e) Human pDC Assay for IFN-α (24 hours) Seq. ID. IFN-α No./ (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 10 μg/ml 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 174.81 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 900.94 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 475.64 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 4813.76 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 15494.15 72 5′-TCTGTCG ₁TTAG-S-GATTG ₁CTGTCT-5′ 1934.09 73 5′-CAGTCG ₁TTCAG-Z-GACTTG ₁CTGAC-5′ 2978.9 74 5′-TCG ₁TCG ₁ACG ₁AT-S-TAG ₁CAG ₁CTG ₁CT-5′ 57697.2 75 5′-TCAGTCG ₁TT AC -X- CA TTG ₁CTGACT-5′ 8171 77 5′- U CAGTCG ₁TTAC-X-CATTG ₁CTGAC U -5′ 598.6 78 5′-TCAGTCG ₁TTAoC-X-CoATTG ₁CTGACT-5′ 4245.4 79 5′-TAGToCG ₂TTTTT-X-TTTTTG ₂CoTGTAT-5′ 2807.2 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 6133.96 81 5′-TAGoToCG ₂TTTTT-X-TTTTTG ₂CoToGTAT-5′ 1028.1 82 5′-TCG ₂oToCG ₂AoCG ₂AT-X-TAG ₂CoAG ₂CoToG ₂CT-5′ 17873.5 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 190.42.1 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 11673.4 86 5′-TCG ₁TCG ₁TTTL-S-LTTTG ₁CTG ₁CT-5′ 10408.2 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 14783.3 89 5′-LTCG ₁TCG ₁TTTL-Z-LTTTG ₁CTG ₁CTL-5′ 6819.14 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 14515.1 92 5′-T C AGTCG ₁TTAC-X-CATTG ₁CTGA C T-5′ 307.8 Media 32.9;  0; 0.105

TABLE IX(f) Human pDC Assay for IL-6 (24 hours) Seq. ID. No./ IL-6 (pg/ml) Oligo No. Sequences and Modification (5′-3′) 10 μg/ml 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 2384.36 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 1405.14 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 2851.75 69 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGCTC-5′ 1598.06 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 1625.8 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 1648.17 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 13805.44 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 19405.66 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 17253.59 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 9277.99 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 5092.34 Media 1847.09; 1918.47

TABLE IX(g) Human pDC Assay for IL-12 (24 hours) Seq. ID. No./ IL-12 (pg/ml) Oligo No. Sequences and Modification (5′-3′) 10 μg/ml 66 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGCTC-5′ 624.29 67 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGCTC-5′ 492.13 68 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGCTC-5′ 724.53 69 5′-CTGTCG ₂TTC UC -X- UC CTTG ₂CTGCTC-5′ 895.07 70 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 369.77 71 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′ 567.95 80 5′-TCTGToCG ₂TTGT-X-TGTTG ₂CoTGTCT-5′ 1498.64 84 5′-TCAGToCG ₂TTAC-S-CATTG ₂CoTGACT-5′ 1604.88 85 5′-TCTGoToCG ₂TAG-Z-GATTG ₂CoToGTCT-5′ 1498.64 88 5′-TCG ₁CG ₁TTTL-Z-LTTTG ₁CTG ₁CT-5′ 1463.20 90 5′-TCG ₁TCG ₁TTTL-X-LTTTG ₁CTG ₁CT-5′ 1417.50 Media 349.26; 397.1

Exemplar TLR9 agonists from Table I were tested for their induction of IL-12 and IL-6 in mouse spleen cell cultures, as described in Example 3. The results shown in Table X(a) and X(b) below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IL-6 and/or IL-12 activation profile in spleen cells and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IL-6 and IL-12 activation.

TABLE X(a) Induction of IL-12 and IL-6 Secretion in Mouse Spleen Cell Cultures Seq. ID. No./ IL-6 (pg/ml ± SD) IL-12 (pg/ml ± SD) Oligo No. Sequence at 1 μg/ml at 3 μg/ml at 1 μg/ml at 3 μg/ml 38 5′-TCTGACG ₁TTCT-Y-TCTTG ₁CAGTCT-5′ 8354 ± 32 24508 ± 86 909 ± 17 876 ± 89 39 5′-TCG ₁AACG ₁TTCG ₁-Y-G ₁CTTG ₁CAAG ₁CT-5′  3371 ± 102 15012 ± 25 621 ± 12 517 ± 19 40 5′-TCG ₁TCG ₁TTCTG-Y-GTCTTG ₁CTG ₁CT-5′ 361 ± 4 4072 ± 1 451 ± 13 279 ± 0  41 5′-TCAGTCGTTAG-Y-GATTGCTGACT-5′ 2496 ± 69 17796 ± 3  856 ± 12 626 ± 6  42 5′-TCTGTCGTTCT-Y-TCTTGCTGTCT-5′ 8034 ± 95 22124 ± 57 659 ± 7  455 ± 18 43 5′-TCGTTGL-Y-LGTTGCT-5′ 3127 ± 22 14412 ± 32 532 ± 11 536 ± 27 47 5′-TCG ₁AACG ₁TTCG ₁-M-TCTTG ₁CTGTCT-5′ 2685 ± 29 15663 ± 35 957 ± 2  566 ± 18 48 5′-TCG ₁AACG ₁TTCG ₁-M-GACAG ₁CTGTCT-5′ 3199 ± 69 17016 ± 11 792 ± 3  528 ± 2  PBS 0.00 0.00  87 ± 16  87 ± 16

TABLE X(b) Induction of IL-12 and IL-6 Secretion in Mouse Spleen Cell Cultures Seq. ID. IL-12 IL-6 No./ (pg/ml ± SD) (pg/ml ± SD) Oligo No. Sequences and Modification (5′-3′) at 1 μg/ml at 1 μg/ml 60 5′-TCTGTCG ₁TTC U o-X-o U CTTG ₁CTGTCT-5′ 4066 ± 47  78 ± 14 61 5′-TCTGTCG ₁TT C o U o-X-o U o C TTG ₁CTGTCT-5′ 2438 ± 81 164 ± 21 62 5′-TCTGTCG ₂TT CU -X- UC TTG ₂CTGTCT-5′ 1782 ± 67 120 ± 36 63 5′-CTGTCG ₂TTC UC -X- CU CTTG ₂CTGTC-5′  2496 ± 105 215 ± 19 64 5′-TCG ₁AACG ₁TT CG -X- GC TTG ₁CAAG ₁CT-5′ 64796 ± 60  3776 ± 25  65 5′-TCG ₁AACG ₁TTCG ₁-L- GA CAG ₁CTGTCT-5′  8245 ± 244 3776 ± 46  Medium  921 ± 60 38 ± 0

Exemplar TLR9 agonists from Table I were tested for their induction of IL-1Ra, IL-6 and IL-112p40p70 in human PBMC cultures, as described in Example 3. The results shown in Table XI below demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides will alter their TLR9 mediated IL-1Rα, IL-6, and IL-12p40p70 activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3′-3′ linked oligonucleotides can be used to increase or decrease IL-1Rα, IL-6, and IL-12p40p70 activation.

TABLE XI IL-1Rα, IL-6 and IL-12p40p70 in human PBMC Seq. ID. No./ Oligo No Sequence IL-1Rα IL-6 IL-12p40p70 43 5′-TCGTTGL-Y-LGTTGCT-5′ 1595.5 1079.5 160.5 44 5′-TCGTTGM-Y-MGTTGCT-5′ 1775.0 931.5 148.0 45 5′-TCG ₁TTGM-Y-MGTTG ₁CT-5′ 954.0 1235.5 71.0 46 5′-TCGTTGM-X-MGTTGCT-5′ 1550.0 800.0 127.0 PBS 187.0 36.0 21.0

As described above, the invention provides, in a first aspect, oligonucleotide-based synthetic agonists of TLR9. Based upon certain chemical modifications to the base, sugar, linkage, or linker, the agonists of TLR9 may possess increased stability when associated, duplexed, with other of the TLR9 agonist molecules, while retaining an accessible 5′-end.

In a second aspect, the invention provides a composition comprising an oligonucleotide-based TLR9 agonist (“a compound”) according to the invention and a physiologically acceptable carrier. The term “physiologically acceptable” generally refers to a material that does not interfere with the effectiveness of the compound and that is compatible with a biological system such as a cell, cell culture, tissue, or organism.

As used herein, the term “carrier” encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material well known in the art for use in physiologically acceptable formulations. It will be understood that the characteristics of the carrier, excipient, or diluent will depend on the route of administration for a particular application. The preparation of physiologically acceptable formulations containing these materials is described in, e.g., Remington's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, Pa., 1990.

The active compound is included in the physiologically acceptable carrier or diluent in an amount sufficient to deliver to a patient a prophylactically or therapeutically effective amount without causing serious toxic effects in the patient treated. The term an “effective amount” or a “sufficient amount” generally refers to an amount sufficient to affect a desired biological effect, such as beneficial results. Thus, an “effective amount” or “sufficient amount” will depend upon the context in which it is being administered. The effective dosage range of the physiologically acceptable derivatives can be calculated based on the weight of the parent compound to be delivered. If the derivative exhibits activity in itself, the effective dosage can be estimated as above using the weight of the derivative, or by other means known to those skilled in the art.

In a third aspect, the invention provides a vaccine. Vaccines according to this aspect comprise a composition according to the invention, and further comprise an antigen. An antigen is a molecule that elicits a specific immune response. Such antigens include, without limitation, proteins, peptides, nucleic acids, carbohydrates and complexes or combinations of any of the same. Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen. Any such antigen may optionally be linked to an immunogenic protein, such as keyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any other immunogenic carrier protein.

Vaccines according to the invention may further include any of the plethora of known adjuvants, including, without limitation, Freund's complete adjuvant, KLH, monophosphoryl lipid A (MPL), alum, and saponins, including QS-21, imiquimod, R848, or combinations thereof.

In a fourth aspect, the invention provides methods for generating a TLR9-mediated immune response in a vertebrate, such methods comprising administering to the vertebrate a compound, composition or vaccine according to the invention. In some embodiments, the vertebrate is a mammal. For purposes of this invention, the term “mammal” is expressly intended to include humans and animals. In preferred embodiments, the compound, composition or vaccine is administered to a vertebrate in need of immune stimulation.

In the methods according to this aspect of the invention, administration of a compound, composition or vaccine according to the invention can be by any suitable route, including, without limitation, parenteral, oral, intratumoral, sublingual, transdermal, topical, intranasal, aerosol, intraocular, intratracheal, intrarectal, mucosal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form. Administration of the compound, composition or vaccine can be carried out using known procedures at dosages and for periods of time effective to reduce symptoms or surrogate markers of the disease. When administered systemically, the compound, composition or vaccine is preferably administered at a sufficient dosage to attain a blood level of a compound according to the invention from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated without serious toxic effects. Preferably, a total dosage of a compound according to the invention ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.

In certain preferred embodiments, a compound, composition or vaccine according to the invention is administered in combination with another agent, including without limitation antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, SiRNA, aptamers, ribozymes, targeted therapies, peptides, proteins, gene therapy vectors, DNA vaccines, and/or adjuvants to enhance the specificity or magnitude of the immune response.

For purposes of this aspect of the invention, the term “in combination with” means in the course of treating a disease or disorder in a patient, administering the compound, composition or vaccine according to the invention and/or the other agent in any order, including simultaneous administration, as well as temporally spaced order of up to several hours, days or weeks apart. Such combination treatment may also include more than a single administration of the compound, composition or vaccine according to the invention, and/or the other agent. The administration of the compound, composition or vaccine according to the invention and/or the other agent may be by the same or different routes.

The methods according to this aspect of the invention are useful for the prophylactic or therapeutic treatment of human or animal disease. For example, the methods are useful for pediatric and veterinary vaccine applications. The methods are also useful for model studies of the immune system.

In a fifth aspect, the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention. In various embodiments, the disease or disorder to be treated is cancer, an autoimmune disorder, infectious disease, airway inflammation, inflammatory disorders, allergy, asthma or a disease caused by a pathogen or allergen. Pathogens include for example bacteria, parasites, fungi, viruses, viroids, and prions. Administration is carried out as described for the fourth aspect of the invention.

The term “treatment” generally refers to an approach intended to obtain a beneficial or desired results, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.

For purposes of the invention, the term “allergy” generally refers to an inappropriate immune response characterized by inflammation and includes, without limitation, food allergies and respiratory allergies. The term “airway inflammation” includes, without limitation, asthma. As used herein, the term “autoimmune disorder” refers to disorders in which “self” components (e.g., proteins) undergo attack by the immune system. Such term includes autoimmune asthma. The term “cancer” includes, without limitation, any malignant growth or tumor caused by abnormal or uncontrolled cell proliferation and/or division. Cancers may occur in humans and/or animals and may arise in any and all tissues. Treating a patient having cancer with the invention may include administration of a compound, composition or vaccine according to the invention such that the abnormal or uncontrolled cell proliferation and/or division is affected.

In a sixth aspect, the invention provides methods for preventing a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention. In various embodiments, the disease or disorder to be prevented is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma or a disease caused by a pathogen. Pathogens include, without limitation, bacteria, parasites, fungi, viruses, viroids, and prions. Administration is carried out as described for the fourth aspect of the invention.

In any of the methods according to the invention, the compound, composition or vaccine according to the invention can be administered in combination with any other agent useful for preventing or treating the disease or condition that does not diminish the immune stimulatory effect of the compound, composition or vaccine according to the invention. In any of the methods according to the invention, the agent useful for preventing or treating the disease or condition includes, but is not limited to, vaccines, antigens, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, TLR agonist, peptides, proteins, gene therapy vectors, DNA vaccines and/or adjuvants to enhance the specificity or magnitude of the immune response, or co-stimulatory molecules such as cytokines, chemokines, protein ligands, trans-activating factors, peptides and peptides comprising modified amino acids. For example, in the prevention and/or treatment of cancer, it is contemplated that the compound, composition or vaccine according to the invention may be administered in combination with a chemotherapeutic compound or a monoclonal antibody. Alternatively, the agent can include DNA vectors encoding for antigen or allergen. In these embodiments, the compound, composition or vaccine according to the invention can variously act as adjuvants and/or produce direct immunomodulatory effects.

The following examples are intended to further illustrate certain preferred embodiments of the invention and are not intended to limit the scope of the invention in any way.

Example 1 Synthesis of Oligonucleotides, Pentane-1,3,5-triol, Pentane-1,5-diol and cis-1,3,5-Cyclohexanetriol Linkers and Functionalization of CPG and OligoPrep Solid Supports

Control pore glass-derivatized 3-methyl-1,3,5-pentanetriol linker (5) was achieved from commercially available 3-methyl-1,3,5-triol 1 as shown in Scheme 1. Initially, bis-DMT protected alcohol 2 was prepared in good yield from 1 by treating with DMTCl in the presence of DMAP. The conventional method of derivatization of CPG was not possible due to the low yields of the succinylation product at 3-hydroxyl of 2, possibly due to steric effects. However, the linker derivatized CPG 5 was prepared by following the alternate approach which eliminates the need for making succinate 3 (Scheme 1). In this route, initially, the CPG beads were activated by treating with 3% trichloroacetic acid (TCA) in dichloromethane (DCM) at room temperature (r.t.) to liberate maximum number of reactive amino groups on the surface of CPG. The activated CPG beads were then derivatized with succinic anhydride in the presence of DMAP to provide CPG beads 4. Finally, CPG derivatized linker 5 was obtained by condensation of 2 with carboxylic groups of CPG 4 in the presence of N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (DEC)/DMAP. After derivatization, the residual carboxylic groups were eliminated by capping reaction with pentachlorophenol.

1,3,5-Pentanetriol linker derivatized CPG 10 and OligoPrep 11 were prepared starting from the commercially available diethyl 3-hydroxy glutarate 6 (Scheme 2). Reduction of 6 with LiAlH₄ yielded 1,3,5-pentanetriol 7 in quantitative yield. The triol 7 was then selectively protected with DMTCl in the presence of DMAP to afford bis-DMT protected alcohol 8, which was then successfully converted into succinate 9, which is ready to load on to the solid support, by treating with succinic anhydride in the presence of DMAP. Attachment of 9 to CPG was accomplished in quantitative loading yield in the presence of DIC/DMAP in pyridine/acetonitrile mixture (10). Whereas, the above protocol gave very poor loading yield in the case of OligoPrep250, a PVA solid support, functionalization. However, quantitative loading yield was achieved in the presence of TBTU/DMAP in acetonitrile (11). The loading was maintained at about ˜40 μmol/g on CPG (10) and ˜125 μmol/g on OligoPrep250 (11) supports, respectively, which increases the nucleotide coupling efficiencies and final yields.

The C5 linker functionalized supports 10 and 11 are ideal for making immunomers with identical sequences. Immunomers with unidentical sequences also exhibited potent immune stimulatory activity in our studies. Appropriately protected C5 linker, such as 14 (Scheme 3), is required in order to make immunomers with unidentical sequences. One of the hydroxyl groups of commercially available 1,5-pentanediol was selectively protected with DMT followed by phosphitylation with 2-cyanoethyl N,N-diisopropylchlorophos-phosphoramidite afforded the required C5 linker 14 (Scheme 3).

We have also focused our attention on the design and development of CpG DNA dendrimers as potent synthetic immune modulatory motifs. In order to make CpG DNA dendrimers, appropriately protected linker phosphoramidites are essential. The C5 linker phosphramidites 15 and 16 were prepared from di-DMT alcohols 2 and 8, respectively, by phosphitylation with 2-cyanoethyl N,N-diisopropylchlorophosphosphoramidite as shown in Scheme 4.

cis-Cyclohexanetriol linker derivatized with CPG 20 was accomplished as shown in Scheme 5. bis-DMT protected cis-1,3,5-cyclohexanetriol 18 was achieved from commercially available cis-1,3,5-cyclohexanetriol (17). The subsequent succinylation of the unprotected hydroxyl of 18 with succinic anhydride in the presence of DMAP afforded desired bis-DMT succinate 19 in 78% yield. Derivatization of CPG with succinate 19 was accomplished in quantitative loading yield (20, 40 μmol/g) in the presence of DIC/DMAP in pyridine/acetonitrile mixture.

Reagents such as diethyl 3-hydroxy glutarate, lithium aluminum hydride (LiAlH₄), 4,4-dimethoxytrityl chloride (DMTCl), 4-dimethylaminopyridine (DMAP), succinic anhydride, O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate (TBTU), N,N′-diisopropylcarbodiimide (DIC), N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (DEC), trichloroacetic acid (TCA), N-methylimidazole (NMI), triethylamine (TEA), diisopropylethylamine (DIPEA) and solvents such as pyridine, dichloromethane (DCM) and tetrahydrofuran (THF) were obtained from Sigma-Aldrich (St. Louis, Mo.) and used without further purification unless mentioned otherwise. Long chain alkyl amine controlled pore glass (CPG; 120-200 mesh, 500 Å, 90-120 μmol/g NH₂ groups) was obtained from CPG Inc. (Lincoln Park, N.J.) and OligoPrep250 was obtained from Merck KGaA (Germany). Cap A (acetic anhydride/2,6-lutidine/THF 1:1:8) and Cap B (N-methylimidazole/THF 16:84) reagents were obtained from Applied Biosystems (Foster City, Calif.). All reactions were performed in glassware which had been oven dried at 120° C. for at least 3 hrs prior to use. TLCs were run on silica gel 60 F₂₅₄ coated on aluminum sheets, and visualized by UV light or by a 5% phosphomolybdic acid (PMA) solution from Sigma-Aldrich (St. Louis, Mo.). Solvents such as ethyl acetate (EtOAc), hexanes, DCM, methanol, t-butyl methyl ether for chromatography were obtained from J. T. Baker and used without purification. Flash column chromatography was performed using silica gel 60 (mesh size 0.040-0.063 mm & 230-400 mesh ASTM) which was obtained from EMD Chemicals (Gibbstown, N.J.). NMR spectra were performed on Varian 400 MHz Unity Inova instrument. Chemical shifts (6) are in ppm relative to TMS and all coupling constants (J) are in Hz.

1,5-Bis-dimethoxytrityloxy-3-methyl-pentan-3-ol (2). DMTCl (3.6 g, 10.5 mmol, 2.1 equiv) in pyridine (25 mL) was added drop wise to an ice cold (0° C.) and stirring solution of 3-methyl-1,3,5-pentanetiol (1, 0.7 g, 5 mmol) and DMAP (0.24 g) in dry pyridine (25 mL) under nitrogen atmosphere. The reaction mixture was allowed to slowly reach room temperature (˜4 h) and continued stirring for overnight. TLC (hexanes/t-butyl methyl ether 2:1 containing 0.5% TEA) indicated the completion of the reaction. Pyridine rotoevaporated to dryness, residue was dissolved in ethyl acetate (250 mL) and washed successively with water (2×100 mL), saturated NH₄Cl solution (2×100 mL), brine (2×100 mL) and water (2×100 mL). Ethyl acetate layer dried over anhydrous MgSO₄ and rotoevaporated to dryness. The residue was purified on silica gel flash column chromatography using hexane/t-butyl methyl ether (3:1) containing 0.5% triethylamine to give bis-DMT product 2 as a white foam (2.9 g, 78%). ¹H-NMR (CDCl3, 400 MHz):

1.56 (

, 3H—CH₃), 1.74-1.79 (m, 4H, —CH₂CHCH₂—), 3.19-3.26 (m, 4H, 1 & 5-CH₂—), 3.78 (d, 12H, —OCH₃), 6.82 (dd, J=8.8, 8H, Ar—H), 7.16-7.40 (m, 18H, Ar—H).

Preparation of bis-DMT-3-methyl-pentanetriol derivatized CPG (5): LCAA-CPG (5 g) was added to 3% TCA (50 mL) and slowly agitated at room temperature for 3 h. The CPG was filtered and washed with 9:1 mixture of TEA/DIPEA (50 mL) followed by DCM (5×100 ml). The activated CPG dried under high vacuum for 1 h. A solution of succinic anhydride (1 g, 10 mmol) and DMAP (0.2 g) in pyridine (30 mL) was added to the above CPG (5 g) and the slurry was shaken at room temperature for 24 hrs. Solutions filtered off and CPG was washed with pyridine (2×25 mL) followed by DCM (5×25 mL) and dried under high vacuum for 2 h to obtain the succinic acid derivative of CPG 4. A solution of di-DMT-3-methyl-pentanetriol 2 (87 mg), DMAP (30 mg), TEA (100 μL) and DEC (0.4 g) in dry pyridine (10 mL) was added to CPG 4 and shaken at room temperature for 15 h. Pentachlorophenol (0.14 g) added to the above mixture and shaken for additional 15 hrs. Solutions filtered off, CPG was thoroughly washed with pyridine (2×25 mL) followed by DCM (5×25 mL) and dried under high vacuum in a desiccator for over night to get Di-DMT-3-methyl-pentanetriol derivatized CPG 5. Loading was determined by treating small portion of CPG with 3% TCA in DCM and assayed DMT content 37 μmol/g) by measuring absorbance at 498 mm.

Synthesis of pentane-1,3,5-triol (7): Diethyl 3-hydroxy glutarate (6, 25 g, 122.4 mmol) in THF (100 mL) was added dropwise to a 1M solution of LiAlH₄ in THF (400 mL) at 0° C. under argon atmosphere with vigorous stirring. After addition, reaction mixture was allowed to reach r. t. (˜4 h) and stirred for overnight. The reaction mixture was cooled to −78° C. (acetone/dry ice bath) and quenched by dropwise addition of saturated NH₄Cl solution (50 mL) giving white precipitate. The reaction mixture was diluted with another 500 mL of THF and white precipitate was filtered through Celite. The precipitate was treated with boiling THF (250 mL) and filtered. The combined organic solution was dried over anhydrous MgSO₄ and solvent removed by rotoevaporation. The residue was purified on a silica gel flash column chromatography using DCM/EtOAc/methanol (6:3:1) affording triol 7 (11.4 g, 95.5 mmol, 78%) as a colorless oil. %). ¹H-NMR (DMSO-d₆, 400 MHz): δ 1.39-1.54 (m, 4H, —CH₂CH(OH)CH₂—), 3.47 (t, J=6.6, 4H, 1 & 5-CH₂—), 3.61-3.68 (m, 1H, —CH(HO)—) and 4.23 (bs, 3H, 1, 3 & 5-OH).

1,5-Bis-[(4,4-dimethoxyphenyl)-phenylmethoxy]-pentan-3-ol (8). DMTCl (16.6 g, 49 mmol, 2.1 equiv) in pyridine (100 mL) was added dropwise to an ice cold (0° C.) and stirring solution of pentanetriol 7 (2.8 g, 23 mmol) and DMAP (2.85 g, 1 equiv) in dry pyridine (50 mL) under argon atmosphere. The reaction mixture was allowed to slowly reach r. t. (˜4 h) and continued stirring for overnight. TLC (hexanes/EtOAc 3:1 containing 0.5% TEA) indicated the completion of the reaction. Pyridine rotoevaporated to dryness, residue was dissolved in DCM (500 mL) and washed successively with water (500 mL), saturated NH₄Cl solution (500 mL), brine (500 mL) and water (2×500 mL). DCM layer dried over anhydrous MgSO₄ and rotoevaporated to dryness. The residue was purified on silica gel flash column chromatography using hexane/EtOAc (3:1) containing 0.5% TEA to give bis-DMT alcohol 8 as a white foam (12.1 g, 16.7 mmol, 72%). ¹H-NMR (CDCl3, 400 MHz): δ 1.65-1.81 (m, 4H, —CH₂CHCH₂—), 3.16-3.31 (m, 4H, DMTO-CH₂—), 3.78 (s, 12H, —OCH₃), 3.95-4.01 (m, 1H, —CH—), 6.81 (d, J=8.8, 8H, Ar—H), 7.17-7.42 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 37.22, 55.38, 61.81, 69.58, 86.54, 113.27, 126.88, 128.01, 128.26, 130.15, 136.44, 145.16, 158.55.

3(1,5-O-Dimethoxytrityl pentanetriol)succinic acid (9): bis-DMT alcohol 8 (12 g, 16.6 mmol) and DMAP (4.04 g, 33.2 mmol) were dissolved in dry pyridine (150 mL) and succinic anhydride (3.31 g, 33.2 mmol) was added portion wise at r.t. with vigorous stirring. The reaction mixture was stirred for over night and pyridine rotoevaporated to dryness. Residue was dissolved in DCM (500 mL) and successively washed with ice cold 10% citric acid solution (2×500 mL) and water (2×500 mL). DCM layer was dried over anhydrous MgSO₄, concentrated to 50 mL volume using rotoevaporator and purified by silica gel flash column chromatography using 0→2% methanol in DCM containing 0.5% TEA to get pure triethylammonium salt of succinate 9 as white foam (11.4 g, 13.8 mmol, 83%). ¹H-NMR (CDCl3, 400 MHz): δ 1.20 (t, J=7.6, 9H, —N(CH₂CH₃)₃), 1.80-1.85 (m, 4H, —CH₂CHCH₂—), 2.40 (s, 4H, —COCH₂CH₂CO—), 2.90 (q, 6H, —N(CH₂CH₃)₃), 3.03-3.11 (m, 4H, 1 & 5-CH₂—), 3.78 (s, 12H, —OCH₃), 5.20-5.26 (m, 1H, —CH—), 6.81 (d, J=8.8, 8H, Ar—H), 7.17-7.42 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 9.09, 30.94, 31.77, 34.45, 45.08, 52.92, 55.32, 59.73, 69.73, 86.00, 113.12, 126.71, 127.85, 128.32, 130.11, 136.54, 145.22, 158.40, 173.07 and 177.71.

Preparation of bis-DMT pentanetriol loaded CPG (10): A solution of succinate 9 (0.83 g, 1 mmol), DMAP (0.4 g, 3.3 mmol) and DIC (5 mL) in 1:6 mixture of pyridine/acetonitrile (105 mL) was added to CPG (25 g) and the slurry was shaken for 24 hrs. Solutions filtered off and CPG was washed with acetonitrile containing 5% pyridine (100 mL) and acetonitrile (250 mL). Cap A (ABI, 89 mL) and Cap B (ABI, 100 mL) solutions were added to CPG support and shaken for 4 h. Solutions filtered off, CPG washed with acetonitrile containing 5% pyridine (2×100 mL) followed by acetonitrile (2×250 mL) and dried under high vacuum for 30 min. A solution of TBDMSCl (5.6 g) and imidazole (1.4 g) in acetonitrile containing 5% pyridine (150 mL) was added to CPG and shaken for 4 h. Solution filtered off, CPG was successively washed with acetonitrile containing 5% pyridine (3×100 mL) and DCM (4×250 mL) and dried under high vacuum in a desiccator for over night to get dry CPG support 10. Loading was determined by treating small portion of CPG with 3% TCA in DCM and assayed DMT content 40 μmol/g) by measuring absorbance at 498 mm.

Preparation of bis-DMT pentanetriol loaded OligoPrep250 (11): OligoPrep250 (100 g preswollen in acetonitrile) was taken in a peptide synthesis vessel and washed with anhydrous acetonitrile (3×100 mL). Succinate 9 (1.752 g, 2.125 mmol), DMAP (1.82 g, 14.87 mmol), TBTU (3.41 g, 10.62 mmol) and acetonitrile (100 mL) were added to OligoPrep250 and the slurry was shaken for 4 hrs. Solution filtered off and OligoPrep was washed with acetonitrile containing 1% TEA (2×100 mL) and acetonitrile (5×100 mL). Cap A (50 mL: NMI/pyridine/acetonitrile=2:3:5) and Cap B (50 mL: acetic anhydride/acetonitrile=1:4) solutions were added to solid support and shaken for 6 hrs. Solutions filtered off, solid support washed with acetonitrile (2×100 mL) and repeated the capping reaction one more time. Solutions filtered off, solid support washed with acetonitrile containing 1% TEA (3×100 mL) followed by acetonitrile (5×100 mL) and dried under high vacuum in a desiccator for 24 hrs to get dry OligoPrep250 support 11 (26.4 g). Loading was determined by treating small portion of OligoPrep with 3% TCA in DCM and assayed DMT content (138 μmol/g) by measuring absorbance at 498 mm.

5-Dimethoxytrityloxy-Pentane-1-ol (13): Pentanediol 12 (12.5 g, 120 mmol) and DMAP (14.6 g, 120 mmol) were dissolved in dry pyridine (100 mL), cooled to −10° C. and maintained under argon atmosphere. DMTCl (37.3 g, 110 mmol, 0.92 equiv) in pyridine (150 mL) was added drop wise with vigorous stirring. The reaction mixture was allowed to slowly reach r.t. (˜4 h) and continued stirring for overnight. Pyridine rotoevaporated to dryness, residue dissolved in DCM (500 mL) and successively washed with water (250 mL), saturated NH₄Cl solution (2×250 mL), brine (250 mL) and water (2×250 mL). DCM layer dried over anhydrous MgSO₄ and rotoevaporated to dryness. The residue was purified by silica gel flash column chromatography using hexanes/EtOAc (3:1) containing 0.5% TEA to give mono-DMT protected alcohol 13 as a colorless syrup (28.2 g, 58%). ¹H-NMR (CDCl3, 400 MHz): δ 1.39-1.47 (m, 2H, —CH₂CH₂CH₂OH), 1.49-1.1.56 (m, 2H, DMTO-CH₂CH₂—), 1.60-1.68 (m, 2H, —CH₂CH₂OH), 3.06 (t, 2H, J=6.2, DMTO-CH₂—), 3.60 (t, 2H, J=6.3, —CH₂OH), 3.77 (s, 12H, —OCH₃), 6.82 (d, J=8.8, 8H, Ar—H), 7.17-7.45 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 22.84, 30.14, 32.92, 55.51, 63.21, 63.57, 85.98, 113.26, 126.87, 128.00, 128.46, 130.30, 136.96, 145.65 and 158.57.

5-Dimethoxytrityloxy-Pentane-1-O-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite (14): To an ice cold solution of 13 (20.32 g, 50 mmol) in anhydrous DCM (500 mL) under nitrogen atmosphere was added DIPEA (26.12 mL, 150 mmol) with vigorous stirring. 2-Cyanoethyl-N,N-diisopropylchlorophosphoramidite (14.2 g, 60 mmol) was then added dropwise followed by NMI (4 mL, 50 mmol). The reaction mixture allowed to slowly reach r.t. in ˜4 h and continued stirring for overnight. TLC in 3:1 hexanes/EtOAc containing 0.5% TEA exhibited the completion of the reaction. The reaction mixture was diluted with another 500 mL of DCM and washed sequentially with saturated aqueous NaHCO₃ (1×500 mL), brine (2×500 mL) and water (1×500 mL). The organic layer dried over anhydrous MgSO₄, filtered and rotoevaporated to dryness. The residue was purified on silica gel flash column chromatography using 3:1 hexane/EtOAc mixture containing 0.5% TEA to get 13 as a colorless viscous liquid (22.3 g, 74%). ¹H-NMR (CDCl3, 400 MHz): δ 1.15 (t, 12H, J=7.6, (Me₂CH)₂N—), 1.37-1.45 (m, 2H, —CH₂CH₂CH₂OP—), 1.52-1.64 (m, 4H, DMTO-CH₂CH₂CH₂CH₂—), 2.55 (t, 2H, J=6.2, —CH₂CN), 3.01 (t, 2H, J=6.5, —CH₂CH₂CN), 3.49-3.64 (m, 4H, DMTO-CH₂— and —CH₂OP—), 3.73 (s, 12H, —OCH₃), 3.71-3.81 (m, 2H, (Me₂CH)₂N—), 6.77 (d, J=8.8, 8H, Ar—H), 7.13-7.41 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 20.56, 20.63, 23.08, 24.82, 24.89, 24.96, 30.05, 31.40, 43.15, 43.27, 55.44, 58.47, 58.66, 63.52, 63.92, 85.89, 113.20, 117.97, 126.81, 127.94, 128.42, 130.25, 136.92, 145.65 and 158.53. ³¹P-NMR: 6145.07.

Synthesis of phosphoramidites 15 and 16: Synthesized using general procedure as described for 14. Compound 15—white foam and yield 69%. ¹H-NMR (CDCl3, 400 MHz): δ 0.89 (d, 6H, J=7, (Me₂CH)₂N—), 1.05 (d, 6H, J=6.4, (Me₂CH)₂N—), 1.25 (s, 3H, —CH₃), 1.88-1.99 (m, 4H, —CH₂CHCH₂—), 2.40 (t, 2H, J=6.4, —CH₂CN), 3.10-3.21 (m, 2H, —OCH₂CH₂CN), 3.30-3.40 (m, 2H, Me₂CH)₂N—), 3.43-3.60 (m, 4H, DMTO-CH₂—), 3.77 (d, 12H, —OCH₃), 6.79 (dd, J=8.8, 8H, Ar—H), 7.17-7.42 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 20.39, 24.27, 24.72, 43.03, 55.38, 57.73, 60.23, 77.96, 78.04, 86.28, 113.15, 118.01, 126.74, 127.89, 128.31, 129.31, 130.18, 136.80, 139.62, 145.47, 158.44. ³¹P-NMR: δ 135.93.

Compound 16—white foam and yield 79%. ¹H-NMR (CDCl3, 400 MHz): δ 1.00 (d, 6H, J=6.4, (Me₂CH)₂N—), 1.10 (d, 6H, J=6.7, (Me₂CH)₂N—), 1.73-1.99 (m, 4H, DMTO-CH₂CH₂CHCH₂—), 2.36 (t, 2H, J=6.6, —CH₂CN), 3.14 (t, 2H, J=6.5, —CH₂CH₂CN), 3.37-3.60 (m, 6H, DMTO-CH₂— and Me₂CH)₂N—), 3.77 (d, 12H, —OCH₃), 4.14-4.22 (m, 1H, —CHOP—), 6.78 (dd, J=8.8, 8H, Ar—H), 7.17-7.42 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 20.38, 24.56, 24.88, 36.82, 43.08, 55.43, 58.39, 60.45, 69.88, 86.09, 113.18, 117.88, 126.81, 127.93, 128.36, 130.20, 136.77, 137.59, 145.47, 158.49. ³¹P-NMR: δ 145.20.

cis-3,5-Bis-dimethoxytrityloxy-cyclohexane-1-ol (18). cis-1,3,5-Cyclohexanetriol dehydrate (5.05 g, 30 mmol) was dissolved in pyridine (100 mL) and rotoevaporated to dryness and dried under high vacuum for 48 hrs to obtain anhydrous cis-1,3,5-cyclohexanetriol (4.05 g, 30.6 mmol). The above anhydrous cyclohexanetriol and DMAP (7.33 g, 60 mmol) were dissolved in dry pyridine (100 mL), cooled in ice bath and maintained under nitrogen atmosphere. DMTCl (20.4 g, 60 mmol, 2 equiv) in dry pyridine (150 mL) was added drop wise to the above solution with vigorous stirring. The reaction mixture was allowed to slowly reach r.t. (˜4 h) and continued stirring for 24 hrs. TLC in 2:1 hexanes/EtOAc mixture containing 0.5% TEA indicated the presence of some starting materials. Reaction mixture stirred five more hrs at 60° C. and pyridine rotoevaporated to dryness. The residue was dissolved in DCM (500 mL) and washed successively with water (500 mL), saturated NH₄Cl solution (500 mL), brine (500 mL) and water (2×500 mL). DCM layer dried over anhydrous MgSO₄ and rotoevaporated to dryness. The residue was purified on silica gel flash column chromatography using 3:1 hexane/EtOAc mixture containing 0.5% TEA to give bis-DMT product 18 as a white solid (8.4 g, 38%). ¹H-NMR (CDCl3, 400 MHz): δ 1.04-1.13 (m, 3H, 2, 4 & 6-CH₂—), 1.24-1.28 (m, 3H, 2, 4 & 6-CH₂—), 1.66 (d, 1H, 1-OH), 2.84-2.93 (m, 1H, —CH—OH), 3.10-3.18 (m, 2H, 3 & 5-CH—), 3.78 (d, 12H, —OCH₃), 6.78 (d, J=8.8, 8H, Ar—H), 7.16-7.42 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 41.42, 42.67, 55.37, 66.16, 67.91, 86.28, 113.12, 126.83, 127.81, 128.53, 130.41, 137.39, 146.29, 158.53.

1(3,5-bis-Dimethoxytrityl-cis-cyclohexanetriol)succinic acid (19): bis-DMT-cyclohexanetriol 18 (4.05 g, 5.5 mmol) and DMAP (1.34 g, 10.1 mmol) were dissolved in dry pyridine (50 mL) and succinic anhydride (1.1 g, 10.1 mmol) was added portion wise at r.t. with vigorous stirring. The reaction mixture was stirred for 48 hrs at r.t. and TLC in DCM containing 2% methanol and 0.5% TEA indicated the complete disappearance of starting material. Pyridine rotoevaporated to dryness, residue dissolved in DCM (250 mL) and successively washed with ice cold 10% citric acid solution (2×250 mL) and water (2×250 mL). DCM layer dried over anhydrous MgSO₄, concentrated to 50 mL volume using rotoevaporator and purified by silica gel flash column chromatography using 0→2% methanol in DCM containing 0.5% TEA to get pure triethylammonium salt of succinate 19 as white foam (3.58 g, 78%). ¹H-NMR (CDCl3, 400 MHz δ 1.17 (t, J=7.6, 9H, —N(CH₂CH₃)₃), 1.17-1.25 (m, 2H, 4-CH₂—), 1.36-1.51 (m, 4H, 2 & 6-CH₂—), 2.37-2.47 (m, 4H, —OCH₂CH₂CN), 2.86 (q, 6H, —N(CH₂CH₃)₃), 2.99-3.10 (m, 2H, 3 & 5-CH—), 3.78 (d, 12H, —OCH₃), 3.98-4.08 (m, 1H, 1-CH—), 6.76 (dd, J=8.8, 8H, Ar—H), 7.15-7.37 (m, 18H, Ar—H). ¹³C NMR (CDCl3, 75.5 MHz): 9.38, 31.16, 31.96, 39.02, 41.76, 45.18, 55.37, 67.68, 86.24, 113.12, 126.79, 127.77, 128.42, 130.33, 130.38, 137.15, 137.26, 146.28, 158.54, 172.58 and 178.16.

Preparation of bis-DMT cyclohexanetriol derivatized CPG 20: A solution of succinate 19 (0.78 g, 0.93 mmol), DMAP (0.38 g, 2.8 mmol) and DIC (3 mL) in 1:7.5 mixture of pyridine/acetonitrile (85 mL) was added to CPG (22.5 g) and the slurry was agitated for 24 hrs. Solutions filtered off and CPG was washed with acetonitrile containing 5% pyridine (2×100 mL) and acetonitrile (3×100 mL). Cap A (ABI, 80 mL) and Cap B (ABI, 90 mL) solutions were added to CPG support and shaken for 4 h. Solutions filtered off, CPG washed with acetonitrile containing 5% pyridine (2×100 mL) followed by acetonitrile (2×250 mL) and dried under high vacuum for 30 min. A solution of TBDMSCl (2.5 g) and imidazole (0.75 g) in acetonitrile containing 5% pyridine (100 mL) was added to CPG and shaken for 5 h. Solution filtered off, CPG was successively washed with acetonitrile containing 5% pyridine (3×100 mL) and DCM (4×100 mL) and dried under high vacuum in a desiccator for over night to get dry CPG support 20. Loading was determined by treating small portion of CPG with 3% TCA in DCM and assayed DMT content 40 μmol/g) by measuring absorbance at 498 mm.

Example 2 Cell Culture Conditions and Reagents, Cytokine Induction by Exemplar Oligos from Table I in HEK293 Cells Expressing Mouse TLR9

HEK293 cells stably expressing mouse TLR9 (Invivogen, San Diego, Calif.) were cultured in 48-well plates in 250 μl/well DMEM supplemented with 10% heat-inactivated FBS in a 5% CO₂ incubator. At 80% confluence, cultures were transiently transfected with 400 ng/ml of SEAP (secreted form of human embryonic alkaline phosphatase) reporter plasmid (pNifty2-Seap) (Invivogen) in the presence of 4 μl/ml of lipofectamine (Invitrogen, Carlsbad, Calif.) in culture medium. Plasmid DNA and lipofectamine were diluted separately in serum-free medium and incubated at room temperature for 5 minutes. After incubation, the diluted DNA and lipofectamine were mixed and the mixtures were incubated at room temperature for 20 minutes. Aliquots of 25 μl of the DNA/lipofectamine mixture containing 100 ng of plasmid DNA and 1 μl of lipofectamine were added to each well of the cell culture plate, and the cultures were continued for 4 hours.

After transfection, medium was replaced with fresh culture medium, exemplar oligos from Table I were added to the cultures, and the cultures were continued for 24 hours. At the end of oligo treatment, 30 μl of culture supernatant was taken from each treatment and used for SEAP assay following manufacturer's protocol (Invivogen). Briefly, culture supernatants were incubated with p-nitrophenyl phosphate substrate and the yellow color generated was measured by a plate reader at 405 nm (Putta M R et al, Nucleic Acids Res., 2006, 34:3231-8).

Example 3 Cytokine Induction by Exemplar Oligos from Table I in Human PBMCs, pDCs, and Mouse Splenocytes Human PBMC Isolation

Peripheral blood mononuclear cells (PBMCs) from freshly drawn healthy volunteer blood (CBR Laboratories, Boston, Mass.) were isolated by Ficoll density gradient centrifugation method (Histopaque-1077, Sigma).

Human pDC Isolation

pDCs were isolated from PBMCs by positive selection using the BDCA4 cell isolation kits (Miltenyi Biotec) according to the manufacturer's instructions.

Mouse Splenocyte Isolation

Spleen cells from 4-8 week old C57BL/6 mice were cultured in RPMI complete medium as described by Zhao, Q., et al (Biochem Pharmacol. 51: 173-182 (1996)) and Branda, R. F., et al (Biochem. Pharmacol. 45: 2037-2043 (1993)). All other culture reagents were purchased from Mediatech (Gaithersburg, Md.).

Cytokine ELISAs

Human PBMCs or mouse splenocytes were plated in 48-well plates using 5×10⁶ cells/ml. Human pDCs were plated in 96-well dishes using 1×10⁶ cells/ml. The exemplar oligos from Table I dissolved in DPBS (pH 7.4; Mediatech) were added to the cell cultures. The cells were then incubated at 37° C. for 24 hr and the supernatants were collected for luminex multiplex or ELISA assays. In certain experiments, the levels of IFN-α, IL-6, and/or IL-12 were measured by sandwich ELISA. The required reagents, including cytokine antibodies and standards, were purchased from PharMingen.

Cytokine Luminex Multiplex

In certain experiments, the levels of IL-1Rα, IL-6, IL-10, IL-12, IFN-α, IFN-γ, MIP-1α, MIP-β, MCP-1, and IL-12p40p70 in culture supernatants were measured by Luminex multiplex assays, which were performed using Biosource human multiplex cytokine assay kits on Luminex 100 instrument and the data were analyzed using StarStation software supplied by Applied Cytometry Systems (Sacramento, Calif.).

Example 4 Human B Cell Proliferation Assay in the Presence of Exemplar Oligos from Table I

Human B cells were isolated from PBMCs by positive selection using the CD19 Cell Isolation Kit (Miltenyi Biotec, Auburn, Calif.) according to the manufacturer's instructions.

The culture medium used for the assay consisted of RPMI 1640 medium supplemented with 1.5 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 50 μM 2-mercaptoethanol, 100 IU/ml penicillin-streptomycin mix and 10% heat-inactivated fetal bovine serum.

A total of 0.5×10⁶ B cells per ml (i.e. 1×10⁵/200 μl/well) were stimulated in 96 well flat bottom plates with different concentrations of exemplar oligos from Table I in triplicate for a total period of 72 hours. After 66 h, cells were pulsed with 0.75 μCi of [³H]-thymidine (1Ci=37 GBq; Perkin Elmer Life Sciences) in 20 μl RPMI 1640 medium (no serum) per well and harvested 6-8 h later. The plates were then harvested using a cell harvester and radioactive incorporation was determined using standard liquid scintillation technique. In some cases the corresponding [³H]-T (cpm) was converted into a proliferation index and reported as such. 

1. A TLR9 agonist having an oligonucleotide as shown in Table I as SEQ. ID. NOs: 1-92, wherein internucleoside linkages are selected from the group consisting of phosphodiester linkages, phosphorothioate linkages and mixtures thereof.
 2. A composition comprising a TLR9 agonist according to claim 1, and further comprising a physiologically acceptable carrier.
 3. A vaccine comprising a composition according to claim 2, and further comprising an antigen.
 4. A method for generating a TLR9-mediated immune response in a vertebrate, comprising administering to the vertebrate an effective amount of a TLR9 agonist according to claim
 1. 5. A method for generating a TLR9-mediated immune response in a vertebrate, comprising administering to the vertebrate an effective amount of a composition according to claim
 2. 6. A method for therapeutically treating a patient having a disease or disorder, comprising administering to the patient a therapeutically effective amount of a TLR9 agonist according to claim
 1. 7. A method for therapeutically treating a patient having a disease or disorder, comprising administering to the patient a therapeutically effective amount of a composition according to claim
 2. 8. A method for therapeutically treating a patient having a disease or disorder, comprising administering to the patient a therapeutically effective amount of a vaccine according to claim
 3. 9. A method for preventing a disease or disorder in a patient that is susceptible to the disease or disorder, comprising administering to the patient a prophylactically effective amount of a TLR9 agonist according to claim
 1. 10. A method for preventing a disease or disorder in a patient that is susceptible to the disease or disorder, comprising administering to the patient a prophylactically effective amount of a composition according to claim
 2. 11. A method for preventing a disease or disorder in a patient that is susceptible to the disease or disorder, comprising administering to the patient a prophylactically effective amount of a vaccine according to claim
 3. 12. The method according to any of claims 4-11, wherein the disease or disorder is selected from the group consisting of cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma and a disease caused by a pathogen. 